CC does not see books on your device that it didn't put on the device. Books in CC's folder that arrive there by some other means (cable, file transfer, copy) will not be in CC's database.
It is possible to add such books to CC's database by asking CC to scan the folders where it stores books whenever you connect to calibre as a wireless device. Click on the menu button, select Settings, Connecting to calibre, Wireless device connection, then "Scan for books on connect" to check the box (it is checked by default). The next time you connect as a wireless device, CC will do the scan and add any new books to its database. It also negotiates with calibre, attempting to match the discovered books with those in the calibre library.
1) CC does not add the books to your calibre library. It does check if the book matches an existing book in your library, and if it does CC will download that book's metadata. If a newly discovered book does not match a book in your library, the metadata for that book in CC will likely be incorrect because it is coming from the book itself.
2) Calibre Companion does not look in folders other than the ones for formats/extensions selected in CC's "Formats and folders" setting. CC also looks only for the formats that it is willing to put in that folder. For example, If mobi and epub files are going into different folders, CC will not scan for mobi files in the epub folder and vice versa. If you are in this situation then you should either combine the folders or move the books to the right folder.
3) If you want to add the book(s) to your calibre library, connect as a wireless device and go to calibre's device view. Right-click on a book and either add the book to calibre's library or match the book with an existing book in calibre's library.
4) Scanning for formats other than epub is very slow. For books other than epub CC must upload the entire book to calibre. If you know which non-epub books in your calibre library are missing from CC's library then it is almost certainly faster to resend them instead of asking CC to do the scan.